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Formation of Human Long Intergenic Non-Coding RNA Genes and Pseudogenes: Ancestral Sequences Are Key Players

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Formation of Human Long Intergenic Non-Coding RNA Genes and Pseudogenes: Ancestral Sequences Are Key Players bioRxiv preprint doi: https://doi.org/10.1101/826784; this version posted October 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Formation of human long intergenic non-coding RNA genes and pseudogenes: ancestral sequences are key players Nicholas Delihas Department of Molecular Genetics and Microbiology Renaissance School of Medicine Stony Brook University Stony Brook, N.Y. USA 11794 Email: [email protected] Key words: gene formation; human long intergenic non-coding RNA genes; pseudogenes; chromosomal segmental duplications; chromosomal 22q11.2 1 bioRxiv preprint doi: https://doi.org/10.1101/826784; this version posted October 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Pathways leading to formation of non-coding RNA and protein genes are varied and complex. We report finding a highly conserved repeat sequence present in both human and chimpanzee genomes that appears to have originated from a common primate ancestor. This sequence is repeatedly copied in human chromosome 22 (chr22) low copy repeats (LCR22) or segmental duplications and forms twenty-one different genes, which include human long intergenic non- coding RNA (lincRNA) gene and pseudogene families, as well as the gamma- glutamyltransferase (GGT) protein gene family and the RNA pseudogenes that originate from GGT sequences. In sharp contrast, only predicted protein genes stem from the homologous repeat sequence present in chr22 of chimpanzee. The data point to an ancestral DNA sequence, highly conserved through evolution and duplicated in humans by chromosomal repeat sequences that serves as a functional genomic element in the development of new and diverse genes in humans and chimpanzee. Introduction Models presented for the pathways in formation of genes are diverse (1). These include formation of long non-coding RNA (lncRNA) genes from protein genes (2-5), with one study based on similarities in open reading frames (5), and the reverse pathway of human protein gene formation from lncRNA genes that are found in rhesus macaque and chimpanzee (6). Here we report new findings on an evolutionarily conserved repeat sequence that is present in multiple and diverse RNA and protein genes and propose that a similar sequence serves as a proto-gene forming unit, a nucleation site for formation of new genes, both non-coding RNA (ncRNA) and protein genes. The repeat sequence is highly prevalent in different segmental duplications or low copy repeats (LCR22) of human chromosome 22 (chr22), specifically in region 22q11.2. Chr22 has the largest number of segmental duplications per unit chromosomal length of any human chromosome (7). These duplications are dynamic (8). Several may have arisen after the separation of human and macaque lineages (9) and they are continuously evolving, as shown by comparisons and differences found in current human populations (10). Segmental duplications have been considered to be important for new gene formation and human evolution (11-13). Additionally, the 22q11.2 region in itself is of special interest as it is prone to genetic deletions formed during fetal development that result in a high rate of genetic abnormalities (14). Segmental duplications have been shown to participate in the deletion process via meiotic nonallelic homologous recombination (9, 11). In this paper we propose a model for the evolutionarily conserved human/chimpanzee repeat sequence and show that it serves as a starting point for formation of new lncRNA genes with subsequent base pair changes, sequence additions and/or deletions. The core sequence consists of the common sequence shared by the gamma-glutamyltransferase (GGT) protein gene family, where GGT is linked to three phylogenetically conserved and distinct sequences. In humans, these sequences form families of long intergenic non-coding RNA genes and pseudogenes that are linked to GGT sequences present in chromosomal segmental duplications; in chimpanzee, the conserved repeat sequence has not been found to form lncRNA genes but to form predicted protein genes. The presence of GGT in the long arm of chr22 was determined several decades ago (15) and its duplication in segmental duplications 2 bioRxiv preprint doi: https://doi.org/10.1101/826784; this version posted October 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. has also been reported (11). The GGT family is well characterized (16, 17). In addition to the GGT-linked gene segments, we describe another protein gene family in LCR22s, the ubiquitin specific peptidase (USP) family that is found linked to lincRNA genes in humans. In chimpanzee, the USP-linked sequences encode only predicted protein genes, which is similar to the findings with GGT–associated sequences. The significance of chromosomal segmental duplications to gene development described here has parallels to the importance of human genome expansion of repeat units in the evolution of regulatory elements (18). Methods Reference genomes for primate species. Homo sapiens chromosome 22, GRCh38.p12 Primary Assembly NCBI was the source of sequences and properties of RNA and protein genes. Pan troglodytes, isolate Yerkes chimp pedigree #C0471 (Clint) chromosome 22, Clint_PTRv2, NCBI was the source of chimpanzee sequences and protein genes. In addition, a cloned sequence from Pan troglodytes, clone rp43-41g5, complete sequence GenBank: AC099533.36 provided an additional copy of the conserved repeat sequence. Gorilla gorilla (western gorilla) chromosome 22, gorGor4, NCBI Reference Sequence: NC_018446.2, locus: NC_018446 (19) was used to search for the presence of GGT genes and the conserved repeat sequence. Gene properties and gene searches. NCBI and Ensembl websites: (https://www.ncbi.nlm.nih.gov/gene) (19-21) and (http://useast.ensembl.org/Homo_sapiens/Info/Index) (22, 23) were used as the primary sources for gene properties. However FAM230A gene annotations provided a partial gene sequence as there is a 50 kbp unsequenced gap within the gene. For, sequence analysis both the FAM230A NMD RNA transcript sequence from NCBI and the FAM230A gene sequence provided by Ensembl was used. Additional databases employed for gene properties were: Gene Cards: GeneCards – the human gene database, (www.genecards.org) (24), HGNC: (Genenames.org) (25), RNAcentral: rnacentral.org/ (26). For chimpanzee gene searches, the NCBI Reference sequence (RefSeq) database was used (19). The NCBI annotation of chimpanzee protein genes are with the Gnomon-The NCBI eukaryotic gene prediction tool (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/gnomon/). Genomic coordinates. The NCBI and Ensembl gene coordinates differ for a number of genes, especially at the 5’ ends. For uniformity, all coordinates used here were according to NCBI with the expectation of AC023490.3 that has been annotated only by Ensembl. The description of linked gene segments in Table 1 is in the order of FAM230-clincRNA-GGT or pseudogenene- GGT. However, in the genome, the gene order for several of the repeat segments is in the reverse orientation. For consistency, all linked genes are shown in the same orientation as in Table 1. Blast, BLAT searches and sequence identity determinations. The Blast search engine (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome (27) and Blat search engine (http://useast.ensembl.org/Homo_sapiens/Tools/Blast?db=core) (22) were both used to find similarities is gene sequences and to initially detect gene families. Nucleotide and amino acid sequence alignments and identity determinations. The EMBL- EBI Clustal Omega Multiple Sequence Alignment program,website: http://www.ebi.ac.uk/Tools/msa/clustalo/ was used for alignment of two or more nucleotide or 3 bioRxiv preprint doi: https://doi.org/10.1101/826784; this version posted October 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. amino acid sequences. This program was also used to determine phylogenetic relationships via generation of a phylogram. The identity between two sequences was determined by the NCBI Basic Local Alignment Search Tools, blastn and blastp, align two or more sequences with the Program Selection: Optimize for Highly similar sequences (megablast) (27). The identities represent only aligned sequences and do not including gaps sequences. RNA expression The expression of RNA from normal tissues were obtained from website: www.ncbi.nlm.nih.gov/gene/, human tissue-specific expression (HPA) RNA-seq normal tissues (28). The expression of circular RNAs: Tissue-specific circular RNA induction during human fetal development was obtained from website: www.ncbi.nlm.nih.gov/gene/ (29) where RNA-seq was performed on 27 different human tissues with samples from 95 individuals. Protein properties. UniProtKB (uniprot.org/uniprot/) was the source of human protein amino acid sequences. For chimpanzee proteins, amino acid sequences and regions of the protein sequence that have predicted functional domains were from: www.ncbi.nlm.nih.gov/protein (20). RepeatMasker analysis of nt sequences. The RepeatMasker program, www.repeatmasker.org/cgi-bin/WEBRepeatMasker (30) was employed to search for transposable elements. The search engine, “hmmer” for DNA sequences and interspersed repeats was used to detect transposable elements. Results Background on GGT-linked gene repeat sequences The DNA repeat sequence was detected in human chr22 segmental duplications LCR22A and LCR22D while analyzing the FAM230 lincRNA genes (31).
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